Here's a page to share important papers, review articles, relevant news, etc.

Some materials from Richard Neher:

Review Articles

• Andersson, Dan I., and Diarmaid Hughes. “Microbiological Effects of Sublethal Levels of Antibiotics.” Nature Reviews Microbiology 12, no. 7 (July 2014): 465–78. doi:10.1038/nrmicro3270.
• Follow up on Daniel's talk: Genetic Draft, selective interference and population genetics of rapid adaptation. Neher, Annual reviews in ecology and evolution.

Tuberculosis genomic diversity papers

• Warner, Digby F., and Valerie Mizrahi. “Complex Genetics of Drug Resistance in Mycobacterium Tuberculosis.” //Nature Genetics// 45
• Farhat, Maha R., et al. “Genomic Analysis Identifies Targets of Convergent Positive Selection in Drug-Resistant Mycobacterium Tuberculosis.” Nature Genetics 45
• Zhang, et al. “Genome Sequencing of 161 Mycobacterium Tuberculosis Isolates from China Identifies Genes and Intergenic Regions Associated with Drug Resistance.” Nature Genetics 45

Books

• antibiotics simplified (med student cheat sheet, richard's office)
• Microbiology: An introduction by Tortara, Funke, Case. (Text book, richard's office)
• Clinical Microbiology made ridiculoulsy simple by Gladwin, Trattler, Mahan (bug parade for medical students)
• 
  

Programming

• Python for biologists

• Code academy (very basic intro into variables, strings, loops etc)

• Canopy (python distribution with IDE and many useful packages)
• Anaconda (alternative distribution, less flashy but as reliable)
• Simple intro into NumPy

Group Assignment

Scripts and dummy data

• HIV reference alignment
• sample of Illumina reads (mapped)
• sample of illumina reads (fastq)
• example script illustrating variable types
• example script highlighting python specific syntax
• basic Luria-Delbrueck simulation
• parse a fasta file

Luria & Delbrück (fluctuation analysis)

Carins et al 1988.pdf

• Details
• Download
• 604 KB

YouTube clip of fluctuation test

Microfluidics

• Protocols

Microscopy